Buggy code:
public boolean isValidInput ( ) { } public boolean hasConaction ( ) { } public void parse ( final File file ) throws FileNotFoundException , IOException , SAXException { } @ Override public void startElement ( final String uri , final String localName , final String qName , final Attributes atts ) throws SAXException { } private boolean parseBranch ( final Attributes atts , final String hrefValue , final String fileName ) { } private boolean searchBrachesMap ( final String id ) { } private void addReferredBranches ( final String hrefValue , final String fileName ) { } @ Override public void endDocument ( ) throws SAXException { } @ Override public void startDocument ( ) throws SAXException { } @ Override public void endElement ( final String uri , final String localName , final String qName ) throws SAXException { } @ Override public InputSource resolveEntity ( final String publicId , final String systemId ) throws IOException , SAXException { } private void parseAttribute ( final Attributes atts , final String attrName ) throws SAXException { String attrValue = atts . getValue ( attrName ) ; String filename = null ; final String attrClass = atts . getValue ( ATTRIBUTE_NAME_CLASS ) ; final String attrScope = atts . getValue ( ATTRIBUTE_NAME_SCOPE ) ; final String attrFormat = atts . getValue ( ATTRIBUTE_NAME_FORMAT ) ; final String attrType = atts . getValue ( ATTRIBUTE_NAME_TYPE ) ; final String codebase = atts . getValue ( ATTRIBUTE_NAME_CODEBASE ) ; if ( attrValue == null ) { return ; } if ( ( ATTRIBUTE_NAME_CONREF . equals ( attrName ) ) || ( ATTRIBUTE_NAME_CONKEYREF . equals ( attrName ) ) ) { hasConRef = true ; } else if ( ATTRIBUTE_NAME_HREF . equals ( attrName ) ) { if ( ( attrClass != null ) && ( PR_D_CODEREF . matches ( attrClass ) ) ) { hasCodeRef = true ; } else { hasHref = true ; } } else if ( ATTRIBUTE_NAME_KEYREF . equals ( attrName ) ) { hasKeyRef = true ; } if ( ( ATTRIBUTE_NAME_KEYS . equals ( attrName ) ) && ( ( attrValue . length ( ) ) != 0 ) ) { String target = atts . getValue ( ATTRIBUTE_NAME_HREF ) ; final String keyRef = atts . getValue ( ATTRIBUTE_NAME_KEYREF ) ; final String copy_to = atts . getValue ( ATTRIBUTE_NAME_COPY_TO ) ; if ( ! ( StringUtils . isEmptyString ( copy_to ) ) ) { target = copy_to ; } if ( target == null ) { target = "" ; } final String temp = target ; for ( final String key : attrValue . split ( "<seq2seq4repair_space>" ) ) { if ( ( ! ( keysDefMap . containsKey ( key ) ) ) && ( ! ( key . equals ( "" ) ) ) ) { if ( ( target != null ) && ( ( target . length ( ) ) != 0 ) ) { if ( ( attrScope != null ) && ( ( attrScope . equals ( "external" ) ) || ( attrScope . equals ( "peer" ) ) ) ) { exKeysDefMap . put ( key , target ) ; keysDefMap . put ( key , new KeyDef ( key , target , null ) ) ; } else { String tail = "" ; if ( ( target . indexOf ( SHARP ) ) != ( - 1 ) ) { tail = target . substring ( target . indexOf ( SHARP ) ) ; target = target . substring ( 0 , target . indexOf ( SHARP ) ) ; } if ( new File ( target ) . isAbsolute ( ) ) { target = FileUtils . getRelativePathFromMap ( rootFilePath , target ) ; } target = FileUtils . normalizeDirectory ( currentDir , target ) ; keysDefMap . put ( key , new KeyDef ( key , ( target + tail ) , null ) ) ; } } else if ( ! ( StringUtils . isEmptyString ( keyRef ) ) ) { keysRefMap . put ( key , keyRef ) ; } else { <START_BUG> keysDefMap . put ( key , new KeyDef ( null , null , null ) ) ; <END_BUG> } } else { final Properties prop = new Properties ( ) ; prop . setProperty ( "%1" , key ) ; prop . setProperty ( "%2" , target ) ; logger . logInfo ( MessageUtils . getMessage ( "DOTJ045I" , prop ) . toString ( ) ) ; } target = temp ; } } if ( ( ( ( "external" . equalsIgnoreCase ( attrScope ) ) || ( "peer" . equalsIgnoreCase ( attrScope ) ) ) || ( ( attrValue . indexOf ( COLON_DOUBLE_SLASH ) ) != ( - 1 ) ) ) || ( attrValue . startsWith ( SHARP ) ) ) { return ; } if ( ( attrValue . startsWith ( "file://" ) ) && ( ( attrValue . indexOf ( "file:////" ) ) == ( - 1 ) ) ) { attrValue = attrValue . substring ( "file://" . length ( ) ) ; if ( UNIX_SEPARATOR . equals ( File . separator ) ) { attrValue = ( UNIX_SEPARATOR ) + attrValue ; } } final File target = new File ( attrValue ) ; if ( ( target . isAbsolute ( ) ) && ( ! ( ATTRIBUTE_NAME_DATA . equals ( attrName ) ) ) ) { attrValue = FileUtils . getRelativePathFromMap ( rootFilePath , attrValue ) ; } else if ( ATTRIBUTE_NAME_DATA . equals ( attrName ) ) { if ( ! ( StringUtils . isEmptyString ( codebase ) ) ) { filename = FileUtils . normalizeDirectory ( codebase , attrValue ) ; } else { filename = FileUtils . normalizeDirectory ( currentDir , attrValue ) ; } } else { filename = FileUtils . normalizeDirectory ( currentDir , attrValue ) ; }

Fix:
keysDefMap . put ( key , new KeyDef ( key , null , null ) ) ;